Antiviral Defense Mechanisms in Archaea

Abstract

Archaea utilize both innate and adaptative immune systems to defend themselves against invasion of mobile genetic elements. The former include the restriction and modification (R-M) systems, abortive infection, and toxin-antitoxin (TA) systems, prokaryotic Argonaute (pAgo), and a most recently identified DNA phosphorothioate modification and virus replication inhibition systems, while the latter, CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system. Due largely to the bloom of CRISPR technology, most antiviral researches are devoted to investigation of the unique prokaryotic adaptative immunity. Archaeal CRISPR-Cas systems characterized thus far include I-A, I-B and I-G of Type I and III-B and III-D, and these systems employ ribonucleoprotein (RNP) complexes that are composed of multiple different Cas proteins to exert nucleic acids interference. Type I systems mediate DNA interference to invading genetic elements and they target the foreign DNA by specifically recognizing a DNA sequence called protospacer-adjacent motif (PAM) on the genetic elements. Type III immune systems confer both RNA and DNA interference, and the DNA interference is transcription dependent. Subsequent characterization of their RNPs has revealed that the system shows three distinct activities: target RNA cleavage at 6 nt periodicity, RNA-activated DNA cleavage and synthesis of cyclic oligoadenylates, a secondary signal that activates Cas-accessary RNases, and the interference is subjected to the spatiotemporal regulation. An outstanding feature of archaeal viruses is that most of them do not lyse host cells in their life cycle. Thus, archaeal viruses constitute good models to investigate how virus-archaeal host interactions have shaped their coevolution.